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Descriptor

Valence

Breadth first search calculating the distance only between boolean atom properties (default: Atom in conjugated environment).

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Breadth First Search (BFS)

The BFS method performs a breadth-first search [clr98] of a graph. -A breadth-first search visits vertices that are closer to the -source before visiting vertices that are further away. In this -context `distance' is defined as the number of edges in the -shortest path from the source vertex. -

Figure 1. Pseudocode for the BFS algorithm

paint all vertices white;
-paint the source grey, set its distance to 0 and enqueue it;
-repeat
-  dequeue vertex v;
-  if v is the target, we're done - exit this algorithm;
-  paint v black;
-  for each white neighbor w of v
-	paint w grey;
-	set distance w to (distance v + 1);
-	set parent w to v;
-	enqueue w
-until the queue is empty
-if we haven't yet exited, we didn't find the target
-The time complexity is [clr98].

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Depth First Search (DFS)

The DFS method performs a depth--first search [clr98] of a graph. -A depth--first search visits vertices that are further to the -source before visiting vertices that are closer away. In this -context `distance' is defined as the number of edges in the -shortest path from the source vertex. -

Figure 1. Pseudocode for the DFS algorithm

DFS(G)
-  {
-    For each v in V,
-    {
-      color[v]=white;
-      pred[u]=NULL
-    }
-
-    time=0;
-    For each u in V
-      If (color[u]=white) DFSVISIT(u)
-  }
-
-
-  DFSVISIT(u)
-  {
-    color[u]=gray;
-    d[u] = ++time;
-
-    For each v in Adj(u)  do
-      If (color[v] = white)
-      {
-        pred[v] = u;
-        DFSVISIT(v);
-      }
-
-    color[u] = black; f[u]=++time;
-  }
-The time complexity is [clr98].

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Topological distance matrix

Calculates the topological distances between all atom pairs. -Here a simple Breadth First Search (BFS ) -is used to calculate these distances, which causes a running time of -O(A3), where -A is the number of atoms.

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Geometrical distance matrix

The geometrical distance matrix calculates the euklidian distance between the 3D coordinates of all atom pairs.

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Morgan: Unique atom numbering

Algorithm to get a unique numbering for molecules (graphs) [mor65]. -

Figure 1. Pseudocode for the Morgan labeling algorithm

label each atom with its degree;
-labels=count the number of different labels;
-hasNTchanged=5;
-for all time
-  label each atom with sum of label+all neighbor labels;
-  actLabels=count the number of different labels;
-  if actLabels equal labels then
-    decrement hasNTchanged;
-    if hasNTchanged is zero break loop;
-  fi
-rof
-The sloppy breaking criteria is necessary, because it's possible that the number of different labels can be -constant for only two iterations. But that's not so interesting, let's continue with the -renumbering part of the Morgan algorithm. As you can see, it's possible, that 'symmetric' atoms in the -molecule will have same labels. Is there now a possibility to solve these 'labeling/renumbering' ties ? -Yes, additional informations, like bond order and element number can be used for resolving renumbering ties -or the suggested Jochum-Gasteiger canonical renumbering [tc00] informations can be used. -

Figure 2. Pseudocode for the Morgan renumbering algorithm

calculate the morgan atom labels;
-start breadth first search from this atom;
-choose node with the highest label and set new atom index to 1;
-repeat
-  build deque i of atoms with same BFS traversing number i;
-  if deque i contains no equal labels
-    renumber atoms in order of decreasing atom labels.
-  fi
-  else
-    try to resolve renumbering tie for the equal labels:
-      1. prefer atom with higher bond order for renumbering
-      2. prefer atom with higher element number for renumbering
-      3. ...
-    if tie solved
-      renumber atoms in order of decreasing atom labels.
-    fi
-    else
-      show renumbering tie warning;
-    esle
-  esle
-  increment i;
-until all atoms are numbered
-The uniquely renumbered molecule can be used to calculate molecule -hashcodes and canonical/unique SMILES representations (see ).

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Bibliography

[bmv84] P. Broto, G. Moreau, and C. Vandycke, Molecular Structures: Perception, Autocorrelation Descriptor and SAR Studies, Eur. J. Med. Chem., 19, 66-70, 1984.

[bs93] B. L. Bush and R. P. Sheridan, PATTY: A Programmable Atom Typer and Language for Automatic Classification of Atoms in Molecular Databases, J. Chem. Inf. Comput. Sci., 33, 756-762, 1993.

[clr98] T. Cormen, C. Leiserson, and R. L. Rivest, 0-262-03141-8, MIT-Press, Introduction to Algorithms, 1998.

[dl93] A. N. Davies and P. Lampen, JCAMP-DX for NMR, Appl. Spec., 47, 1093-1099, 1993.

[dw88] R. S. Mc Donald and P. A. Wilks, JCAMP-DX: A Standard Form for Exchange of Infrared Spectra in Computer Readable Form, Appl. Spec., 42, 151-162, 1988.

[ers00] P. Ertl, B. Rohde, and P. Selzer, Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties, J. Med. Chem., 43, 3714-3717, 2000.

[fig96] J. Figueras, Ring Perception Using Breadth-First Search, J. Chem. Inf. Comput. Sci., 36, 986-991, 1996.

[gas95] J. Gasteiger, Keyword Reference Manual for Gasteiger Clear Text Files.

[gbt02] A. Golbraikh, D. Bonchev, and A. Tropsha, Novel Z/E-Isomerism Descriptors Derived from Molecular Topology and Their Application to QSAR Analysis, J. Chem. Inf. Comput. Sci., 42, 769-787, 2002.

[ghhjs91] J. Gasteiger, B. M. Hendriks, P. Hoever, C. Jochum, and H. Somberg, JCAMP-CS: A Standard Format for Chemical Structure Information in Computer Readable Form, Appl. Spec., 45, 4-11, 1991.

[gm78] J. Gasteiger and M. Marsili, A New Model for Calculating Atomic Charges in Molecules, Tetrahedron Lett., ?, 3181-3184, 1978.

[gt03] A. Golbraikh and A. Tropsha, QSAR Modeling Using Chirality Descriptors Derived from Molecular Topology, J. Chem. Inf. Comput. Sci., 42, 144-154, 2003.

[gxsb00] L. Xue, F. L. Stahura, J. W. Godden, and J. Bajorath, Searching for molecules with similar biological activity: analysis by fingerprint profiling, Pac. Symp. Biocomput., 8, 566-575, 2000.

[lhdl94] P. Lampen, H. Hillig, A. N. Davies, and M. Linscheid, JCAMP-DX for Mass Spectrometry, Appl. Spec., 48, 1545-1552, 1994.

[mor65] H. L. Morgan, The Generation of a Unique Machine Description for Chemical Structures - A Technique Developed at Chemical Abstracts Service, J. Chem. Doc., 5, 107-113, 1965.

[mr99] P. Murray-Rust and H. S. Rzepa, Chemical Markup, XML, and the Worldwide Web. 1. Basic Principles, J. Chem. Inf. Comput. Sci., 39, 928-942, 1999.

[mr01a] P. Murray-Rust and H. S. Rzepa, Chemical Markup, XML and the World-Wide Web. 2. Information Objects and the CMLDOM, J. Chem. Inf. Comput. Sci., 41, ?-?, 2001.

[mr01b] G. V. Gkoutos, P. Murray-Rust, H. S. Rzepa, and M. Wright, Chemical markup, XML, and the world-wide web. 3. toward a signed semantic chemical web of trust, J. Chem. Inf. Comput. Sci., 41, 1295-1300, 2001.

[sdf] Inc. MDL Information Systems, Structured Data File format.

[smarts] Inc. Daylight Chemical Information Systems, Smiles ARbitrary Target Specification (SMARTS).

[smiles] Inc. Daylight Chemical Information Systems, Simplified Molecular Input Line Entry System (SMILES).

[tc00] R. Todeschini and V. Consonni, 3-52-29913-0, Wiley-VCH, Handbook of Molecular Descriptors.

[wc99] S. A. Wildman and G. M. Crippen, Prediction of Physicochemical Parameters by Atomic Contributions, J. Chem. Inf. Comput. Sci., 39, 868-873, 1999.

[wei88] D. Weinenger, SMILES: a Chemical Language for Information Systems. 1. Introduction to Methodology and Encoding Rules, J. Chem. Inf. Comput. Sci., 28, 31-36, 1988.

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Descriptor

Atom property breadth first search

Breadth first search calculating the distance only between boolean atom properties (default: Atom in conjugated environment).

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Descriptor

Atom property distance matrix

Distance matrix calculating the distance only between boolean atom properties (default: Atom in conjugated environment).

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Descriptor

Number of acidic groups

Number of acidic groups.

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Descriptor

Number of aliphatic hydroxy groups

Number of aliphatic hydroxy groups.

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Descriptor

Number of aromatic bonds

Number of aromatic bonds.

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Descriptor

Number of Hydrogen Bond Donors (HBD)

Number of Hydrogen Bond Donors (HBD). The default SMARTS pattern is: [!#6;!H0].

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Descriptor

Atom in acceptor

Is this atom a hydrogen acceptor atom.

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Descriptor

Atom in conjugated environment

Atom in conjugated environment. -

Table 1. SMARTS definitions for assigning the conjugated atom property flag

SMARTSDescription
aAromatic atoms
*=,#*-,=*=,#*All butadien analogues
[N,P,O,S]=,#*-[*;!H0]alpha, beta unsaturated (pi effect)
*=,#*-[F,Cl,Br,I]alpha, beta unsaturated (sigma effect)
*=,#*-[N,P,O,S;!H0]alpha, beta unsaturated (pi effect, tautomer)

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Descriptor

Atom in donor or acceptor

Is this atom a hydrogen donor or acceptor atom.

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Descriptor

Atom in donor

Is this atom a hydrogen donor atom.

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Descriptor

Atom in ring

Is this atom a ring atom.

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Descriptor

Atom is terminal carbon

Is this atom a terminal carbon atom.

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Descriptor

Atom is negative

Is this atom a negative charged atom.

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Descriptor

Atom is positive

Is this atom a positive charged atom.

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Descriptor

Atom masss

Atom mass.

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Descriptor

Valence

Valence.

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Descriptor

Van der Waals volume

Van der Waals volume.

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Descriptor

Moreau-Broto topological autocorrelation

Moreau-Broto topological autocorrelation [bmv84]. -

Equation 1. Moreau-Broto autocorrelation

-where dij is the topological distance between the atoms -i and atom j, wi -and wj are the atom properties of the atoms i and -j.

It must be mentioned that the autocorrelation is only a special case of the radial distribution function ().

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Descriptor

Number of basic groups

Number of basic groups.

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\ No newline at end of file diff --git a/java/docs/feature/BondInAromaticSystem.html b/java/docs/feature/BondInAromaticSystem.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/BondInAromaticSystem.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/BondInRing.html b/java/docs/feature/BondInRing.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/BondInRing.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/BondIsAmide.html b/java/docs/feature/BondIsAmide.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/BondIsAmide.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/BondIsCarbonyl.html b/java/docs/feature/BondIsCarbonyl.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/BondIsCarbonyl.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/BondIsClosure.html b/java/docs/feature/BondIsClosure.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/BondIsClosure.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/BondIsEster.html b/java/docs/feature/BondIsEster.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/BondIsEster.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/BondIsPrimaryAmide.html b/java/docs/feature/BondIsPrimaryAmide.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/BondIsPrimaryAmide.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/BondIsRotor.html b/java/docs/feature/BondIsRotor.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/BondIsRotor.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/BondKekuleType.html b/java/docs/feature/BondKekuleType.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/BondKekuleType.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/BurdenEigenvalues.html b/java/docs/feature/BurdenEigenvalues.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/BurdenEigenvalues.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/BurdenModifiedEigenvalues.html b/java/docs/feature/BurdenModifiedEigenvalues.html deleted file mode 100644 index dc6a83b..0000000 --- a/java/docs/feature/BurdenModifiedEigenvalues.html +++ /dev/null @@ -1,96 +0,0 @@ -

Descriptor

Burden modified eigenvalues

Burden modified eigenvalues [tc00].

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\ No newline at end of file diff --git a/java/docs/feature/CompressedFeatureMatrix.html b/java/docs/feature/CompressedFeatureMatrix.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/CompressedFeatureMatrix.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/ConjElectroTopolState.html b/java/docs/feature/ConjElectroTopolState.html deleted file mode 100644 index bc0369e..0000000 --- a/java/docs/feature/ConjElectroTopolState.html +++ /dev/null @@ -1,173 +0,0 @@ -

Descriptor

Conjugated electrotopological state

Conjugated electrotopological state [wz03,wfz04b]. -

Equation 1. Conjugated electrotopological state

-Ii is the intrinsic state of atom i () -and k the distance influence. The distance influence is reduced by the conjugated topological distance -

Equation 2. Conjugated topological distance

-where Ci is the conjugated atom i () -of the molecule.

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\ No newline at end of file diff --git a/java/docs/feature/ConjugatedTopologicalDistance.html b/java/docs/feature/ConjugatedTopologicalDistance.html deleted file mode 100644 index 6deea0d..0000000 --- a/java/docs/feature/ConjugatedTopologicalDistance.html +++ /dev/null @@ -1,117 +0,0 @@ -

Descriptor

Conjugated topological distance

Conjugated topological distance [wz03,wfz04b]. -

Equation 1. Conjugated topological distance

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\ No newline at end of file diff --git a/java/docs/feature/DistanceDistanceMatrix.html b/java/docs/feature/DistanceDistanceMatrix.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/DistanceDistanceMatrix.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/DistanceMatrix.html b/java/docs/feature/DistanceMatrix.html deleted file mode 100644 index ecd0533..0000000 --- a/java/docs/feature/DistanceMatrix.html +++ /dev/null @@ -1,111 +0,0 @@ -

Descriptor

Topological distance matrix

Calculates the topological distances between all atom pairs. -Here a simple BFS (see also ) -is used to calculate these distances, which causes a running time of -O(A3), where -A is the number of atoms.

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Descriptor

Electrogeometrical state

Electrogeometrical state [wz03,wfz04b]. -

Equation 1. Electrogeometrical state

-Ii is the intrinsic state of atom i () -and k the distance influence.

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\ No newline at end of file diff --git a/java/docs/feature/ElectrotopologicalState.html b/java/docs/feature/ElectrotopologicalState.html deleted file mode 100644 index 6de0bf2..0000000 --- a/java/docs/feature/ElectrotopologicalState.html +++ /dev/null @@ -1,139 +0,0 @@ -

Descriptor

Electrotopological state

Electrotopological state [tc00,wfz04b]. -

Equation 1. Electrotopological state

-Ii is the intrinsic state of atom i () -and k the distance influence.

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\ No newline at end of file diff --git a/java/docs/feature/FractionRotatableBonds.html b/java/docs/feature/FractionRotatableBonds.html deleted file mode 100644 index a34080c..0000000 --- a/java/docs/feature/FractionRotatableBonds.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Fraction of rotatable bonds

Fraction of rotatable bonds.

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\ No newline at end of file diff --git a/java/docs/feature/GeomDistanceMatrix.html b/java/docs/feature/GeomDistanceMatrix.html deleted file mode 100644 index ff8cc05..0000000 --- a/java/docs/feature/GeomDistanceMatrix.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Geometrical distance matrix

The geometrical distance matrix calculates the euklidian distance between the 3D coordinates of all atom pairs.

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Descriptor

Geometrical diameter

Geometrical diameter.

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Descriptor

Geometrical radius

Geometrical radius.

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Descriptor

Geometrical shape coefficient

Geometrical shape coefficient.

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\ No newline at end of file diff --git a/java/docs/feature/GlobalTopologicalChargeIndex.html b/java/docs/feature/GlobalTopologicalChargeIndex.html deleted file mode 100644 index 63e2715..0000000 --- a/java/docs/feature/GlobalTopologicalChargeIndex.html +++ /dev/null @@ -1,96 +0,0 @@ -

Descriptor

Global topological charge

Global topological charge [tc00].

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\ No newline at end of file diff --git a/java/docs/feature/GraphPotentials.html b/java/docs/feature/GraphPotentials.html deleted file mode 100644 index a192e96..0000000 --- a/java/docs/feature/GraphPotentials.html +++ /dev/null @@ -1,131 +0,0 @@ -

Descriptor

Graph potentials

Graph potentials [wy96] or rotational symmetry descriptor. Only the connection table -is needed to calculate the external rotational symmetry, or topological equivalent atoms. -

Equation 1. Graph potentials

-where vi is the valence (vertex degree) of the atom -i.

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\ No newline at end of file diff --git a/java/docs/feature/GraphShapeCoefficient.html b/java/docs/feature/GraphShapeCoefficient.html deleted file mode 100644 index 735e913..0000000 --- a/java/docs/feature/GraphShapeCoefficient.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Graph shape coefficient

Graph shape coefficient.

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Descriptor

Number of Hydrogen Bond Acceptors (HBA) 1

Number of Hydrogen Bond Acceptors (HBA) 1. -The default SMARTS pattern is: [$([!#6;+0]);!$([F,Cl,Br,I]);!$([o,s,nX3]);!$([Nv5,Pv5,Sv4,Sv6])].

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Descriptor

Number of Hydrogen Bond Acceptors (HBA) 2

Number of Hydrogen Bond Acceptors (HBA) 2. -The default SMARTS pattern is: [$([$([#8,#16]);!$(*=N~O);!$(*~N=O);X1,X2]),$([#7;v3;!$([nH]);!$(*(-a)-a)])].

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Descriptor

Number of Hydrogen Bond Donors (HBD) 1

Number of Hydrogen Bond Donors (HBD) 1. The default SMARTS pattern is: [!#6;!H0].

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Descriptor

Number of Hydrogen Bond Donors (HBD) 2

Number of Hydrogen Bond Donors (HBD) 2. -The default SMARTS pattern is: [$([O;H1,-&!$(*-N=O)]),$([S;H1&X2,-&X1]),$([#7;H;!$(*(S(=O)=O)C(F)(F)F);!$(n1nnnc1);!$(n1nncn1)]),$([#7;-])].

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\ No newline at end of file diff --git a/java/docs/feature/HeavyBonds.html b/java/docs/feature/HeavyBonds.html deleted file mode 100644 index c460fba..0000000 --- a/java/docs/feature/HeavyBonds.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Number of heavy bonds

Number of heavy bonds.

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\ No newline at end of file diff --git a/java/docs/feature/HeteroCycles.html b/java/docs/feature/HeteroCycles.html deleted file mode 100644 index d1e124f..0000000 --- a/java/docs/feature/HeteroCycles.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Number of heterocycles

Number of heterocycles.

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\ No newline at end of file diff --git a/java/docs/feature/HydrophobicGroups.html b/java/docs/feature/HydrophobicGroups.html deleted file mode 100644 index 020d78c..0000000 --- a/java/docs/feature/HydrophobicGroups.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Number of hydrophobic groups

Number of hydrophobic groups.

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\ No newline at end of file diff --git a/java/docs/feature/IntrinsicState.html b/java/docs/feature/IntrinsicState.html deleted file mode 100644 index 82c8c76..0000000 --- a/java/docs/feature/IntrinsicState.html +++ /dev/null @@ -1,145 +0,0 @@ -

Descriptor

Intrinsic topological state

Intrinsic topological state [tc00,wfz04b]. -

Equation 1. Intrinsic topological state

-where Li is the principal quantum number, - is the number of valence electrons, and - is the number of sigma electrons of the -ith atom ai.

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Descriptor

Kier Shape 1

The Kier shape - descriptor [tc00] -can be defined as :

Equation 1. Kier shape 1

Pmax is the maximum number of paths of length 1. -Pmin is the minimum number of paths of length 1 in a molecule graph of same -atom number. -P1 is the number of paths in the given molecule of length 1. -or:

Equation 2. Kier shape 1 (alternative formulation)

A means the number of nodes in the molecules graph. -P1 is the number of paths of length 1 in the given molecule.

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Descriptor

Kier shape 2

The Kier shape - descriptor [tc00] -can be defined as :

Equation 1. Kier shape 2

A means the number of nodes in the molecules graph. -P2 is the number of paths of length 2 in the given molecule.

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Descriptor

Kier shape 3

The Kier shape - descriptor [tc00] -can be defined as :

Equation 1. Kier shape 3

A means the number of nodes in the molecules graph. -P3 is the number of paths of length 3 in the given molecule.

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\ No newline at end of file diff --git a/java/docs/feature/LogP.html b/java/docs/feature/LogP.html deleted file mode 100644 index 914533b..0000000 --- a/java/docs/feature/LogP.html +++ /dev/null @@ -1,96 +0,0 @@ -

Descriptor

Octanol/Water partition coefficient (logP)

Octanol/Water partition coefficient (logP) or hydrophobicity [wc99].

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Descriptor

Molar refractivity (MR)

Molar refractivity (MR) [wc99].

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\ No newline at end of file diff --git a/java/docs/feature/MolecularWeight.html b/java/docs/feature/MolecularWeight.html deleted file mode 100644 index e463e1c..0000000 --- a/java/docs/feature/MolecularWeight.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Molecular weight (MW)

Molecular weight (MW).

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\ No newline at end of file diff --git a/java/docs/feature/MoleculeHashcode.html b/java/docs/feature/MoleculeHashcode.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/MoleculeHashcode.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/NO2Groups.html b/java/docs/feature/NO2Groups.html deleted file mode 100644 index 6fa91d4..0000000 --- a/java/docs/feature/NO2Groups.html +++ /dev/null @@ -1,97 +0,0 @@ -

Descriptor

Number of -NO2 groups

Number of -NO2 groups.

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\ No newline at end of file diff --git a/java/docs/feature/NumberOfAtoms.html b/java/docs/feature/NumberOfAtoms.html deleted file mode 100644 index f79063f..0000000 --- a/java/docs/feature/NumberOfAtoms.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Number of atoms

Number of atoms.

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Descriptor

Number of boron atoms

Number of boron atoms.

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Descriptor

Number of bonds

Number of bonds.

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\ No newline at end of file diff --git a/java/docs/feature/NumberOfBr.html b/java/docs/feature/NumberOfBr.html deleted file mode 100644 index 5807bb9..0000000 --- a/java/docs/feature/NumberOfBr.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Number of bromine atoms

Number of bromine atoms.

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\ No newline at end of file diff --git a/java/docs/feature/NumberOfC.html b/java/docs/feature/NumberOfC.html deleted file mode 100644 index a1b224e..0000000 --- a/java/docs/feature/NumberOfC.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Number of carbon atoms

Number of carbon atoms.

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Descriptor

Number of chlorine atoms

Number of chlorine atoms.

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Descriptor

Number of fluorine atoms

Number of fluorine atoms.

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\ No newline at end of file diff --git a/java/docs/feature/NumberOfHal.html b/java/docs/feature/NumberOfHal.html deleted file mode 100644 index 11df356..0000000 --- a/java/docs/feature/NumberOfHal.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Number of halogen atoms

Number of halogen atoms.

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\ No newline at end of file diff --git a/java/docs/feature/NumberOfI.html b/java/docs/feature/NumberOfI.html deleted file mode 100644 index 0580e12..0000000 --- a/java/docs/feature/NumberOfI.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Number of iodine atoms

Number of iodine atoms.

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\ No newline at end of file diff --git a/java/docs/feature/NumberOfN.html b/java/docs/feature/NumberOfN.html deleted file mode 100644 index bd65ada..0000000 --- a/java/docs/feature/NumberOfN.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Number of nitrogen atoms

Number of nitrogen atoms.

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\ No newline at end of file diff --git a/java/docs/feature/NumberOfO.html b/java/docs/feature/NumberOfO.html deleted file mode 100644 index 7ecbe0a..0000000 --- a/java/docs/feature/NumberOfO.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Number of oxygen atoms

Number of oxygen atoms.

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\ No newline at end of file diff --git a/java/docs/feature/NumberOfP.html b/java/docs/feature/NumberOfP.html deleted file mode 100644 index 3669e91..0000000 --- a/java/docs/feature/NumberOfP.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Number of phosphorus atoms

Number of phosphorus atoms.

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\ No newline at end of file diff --git a/java/docs/feature/NumberOfS.html b/java/docs/feature/NumberOfS.html deleted file mode 100644 index b735ee5..0000000 --- a/java/docs/feature/NumberOfS.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Number of sulfur atoms

Number of sulfur atoms.

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\ No newline at end of file diff --git a/java/docs/feature/OSOGroups.html b/java/docs/feature/OSOGroups.html deleted file mode 100644 index ca49ebf..0000000 --- a/java/docs/feature/OSOGroups.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Number of -OSO atoms

Number of -OSO atoms.

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\ No newline at end of file diff --git a/java/docs/feature/PolarSurfaceArea.html b/java/docs/feature/PolarSurfaceArea.html deleted file mode 100644 index 357056f..0000000 --- a/java/docs/feature/PolarSurfaceArea.html +++ /dev/null @@ -1,96 +0,0 @@ -

Descriptor

Polar surface area (PSA)

Polar surface area (PSA) [ers00].

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Descriptor

Radial distribution function (RDF)

The radial distribution function (RDF) [msg99,wfz04b] can be interpreted as the probability distribution of finding an atom in a spherical volume of -radius r. -

Equation 1. Radial distribution function

-where rij is the geometrical distance between the atoms -i and atom j, wi -and wj are the atom properties of the atoms i and -j. B is the smoothing parameter -(fuzziness of the distance rij) for the interatomic distance and -f the scaling factor.

If B aims to infinity the RDF code approximates to the autocorrelation function () and the fuzziness -of the distance rij vanishes. So the RDF code can be treated as a generalized -autocorrelation function.

The RDF user parameters can be defined in the joelib.properties-file, otherwise the default parameters will be used:

jcompchem.joelib.desc.types.RadialDistributionFunction.minSphericalVolume = 0.2
-joelib.desc.types.RadialDistributionFunction.maxSphericalVolume = 10.0
-joelib.desc.types.RadialDistributionFunction.sphericalVolumeResolution = 0.2
-joelib.desc.types.RadialDistributionFunction.smoothingFactor = 25

Optional the RDF can be calculated with protonated molecules, but you must be sure that all available atom -properties are calculated with hydrogens also. Because this is not the standard, this option should be only used by developers.

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Descriptor

Number of rotatable bonds

Number of rotatable bonds, where the atoms are heavy atoms with bond order one and a hybridization which is not one (no sp). -Additionally the bond is a non-ring-bond.

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\ No newline at end of file diff --git a/java/docs/feature/SMILESMolecule.html b/java/docs/feature/SMILESMolecule.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/SMILESMolecule.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/SO2Groups.html b/java/docs/feature/SO2Groups.html deleted file mode 100644 index e4cd9a7..0000000 --- a/java/docs/feature/SO2Groups.html +++ /dev/null @@ -1,97 +0,0 @@ -

Descriptor

Number of -SO2 atoms

Number of -SO2 atoms.

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Descriptor

Number of -SO groups

Number of -SO groups.

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Descriptor

Pharmacophore fingerprint

Pharmacophore fingerprint [gxsb00]. -

Table 1. Pharmacophore fingerprint definition

Bit positionSet when
1Fraction of rotatable bonds > 0.0
2Fraction of rotatable bonds > 0.1
3Fraction of rotatable bonds > 0.2
4Fraction of rotatable bonds > 0.3
5Fraction of rotatable bonds > 0.4
6Aromatic bonds in molecule > 2
7Aromatic bonds in molecule > 8
8Aromatic bonds in molecule > 16
9Aromatic bonds in molecule > 20
10Aromatic bonds in molecule > 26
11Aromatic bonds in molecule > 32
12Aromatic bonds in molecule > 38
13Molecule contains a heterocycle
14Molecule contains an aromatic hydroxy group
15Molecule contains an aliphatic hydroxy group
16Molecule contains an aliphatic secondary amine
17Molecule contains an aliphatic tertiary amine
18Molecule contains a phenyl ring
19Molecule contains a ring containing nitrogen
20Molecule contains a -SO2 group
21Molecule contains a -SO
22Molecule contains an ester
23Molecule contains an amide
24Molecule contains a 5-membered non-aromatic ring
25Molecule contains a 5-membered aromatic ring
26Molecule contains a 9-membered or larger (fused) ring
27Molecule contains a fused ring system
28Molecule contains a fused aromatic ring system
29Molecule contains a -OSO group
30Molecule contains a halogen atom
31Molecule contains a nitrogen atom attached to alpha-carbon of aromatic system
32Molecule contains a -NO2 group
33Molecule contains rings separated by 2-3 non-ring atoms
34Molecule contains rings separated by 4-5 non-ring atoms
35Molecule contains a NN group
36Molecule contains a carbon atom attached to 3 carbons and a hetero atom
37Molecule contains an oxygen atom separated by 2 atoms
38Molecule contains a methyl group attached to hetero atom
39Molecule contains a double bond
40Molecule contains a non-H atom linked to 3 heteroatoms
41Molecule contains a quaternary atom
42Molecule contains 2 methylenes separated by 2 atoms
43Molecule contains a non-ring oxygen atom attached to aromatic system
44Molecule contains 2 non-C,H atoms separated by 2 atoms
45Number of hydrogen bond acceptors >= 1
46Number of hydrogen bond acceptors >= 2
47Number of hydrogen bond acceptors >= 3
48Number of hydrogen bond acceptors >= 4
49Number of hydrogen bond acceptors >= 5
50Number of hydrogen bond acceptors >= 6
51Number of hydrogen bond acceptors >= 7
52Number of hydrogen bond acceptors >= 8
53Number of hydrogen bond acceptors >= 9
54Number of hydrogen bond acceptors >= 10

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Descriptor

Valence

Atom pair descriptor using topological distances.

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Descriptor

Topological diameter

Topological diameter.

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  Bibliography
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Descriptor

Topological radius

Topological radius.

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  Bibliography
\ No newline at end of file diff --git a/java/docs/feature/WeightedBurdenEigenvalues.html b/java/docs/feature/WeightedBurdenEigenvalues.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/WeightedBurdenEigenvalues.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/WeightedBurdenModifiedEigenvalues.html b/java/docs/feature/WeightedBurdenModifiedEigenvalues.html deleted file mode 100644 index 0e93938..0000000 --- a/java/docs/feature/WeightedBurdenModifiedEigenvalues.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Weighted burden modified eigenvalues

Accepts six different weighted atom properties to calculate BCUT values.

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  Bibliography
\ No newline at end of file diff --git a/java/docs/feature/ZagrebIndex1.html b/java/docs/feature/ZagrebIndex1.html deleted file mode 100644 index 130990f..0000000 --- a/java/docs/feature/ZagrebIndex1.html +++ /dev/null @@ -1,123 +0,0 @@ -

Descriptor

Zagreb index 1

Zagreb index 1 [tc00].

Equation 1. Zagreb index 1

where a are all atoms of the hydrogen depleted graph and - is the vertex degree.

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  Bibliography
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Descriptor

Zagreb index 2

Zagreb index 2 [tc00].

Equation 1. Zagreb index 2

where b are all bonds of the hydrogen depleted graph and - is the vertex degree. -i and j are the atom indices -of the atoms connected to the bond b.

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  Bibliography
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Prev 

Bibliography

[bmv84] P. Broto, G. Moreau, and C. Vandycke, Molecular Structures: Perception, Autocorrelation Descriptor and SAR Studies, Eur. J. Med. Chem., 19, 66-70, 1984.

[bs93] B. L. Bush and R. P. Sheridan, PATTY: A Programmable Atom Typer and Language for Automatic Classification of Atoms in Molecular Databases, J. Chem. Inf. Comput. Sci., 33, 756-762, 1993.

[clr98] T. Cormen, C. Leiserson, and R. L. Rivest, 0-262-03141-8, MIT-Press, Introduction to Algorithms, 1998.

[dl93] A. N. Davies and P. Lampen, JCAMP-DX for NMR, Appl. Spec., 47, 1093-1099, 1993.

[dw88] R. S. Mc Donald and P. A. Wilks, JCAMP-DX: A Standard Form for Exchange of Infrared Spectra in Computer Readable Form, Appl. Spec., 42, 151-162, 1988.

[ers00] P. Ertl, B. Rohde, and P. Selzer, Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties, J. Med. Chem., 43, 3714-3717, 2000.

[fig96] J. Figueras, Ring Perception Using Breadth-First Search, J. Chem. Inf. Comput. Sci., 36, 986-991, 1996.

[gas95] J. Gasteiger, Keyword Reference Manual for Gasteiger Clear Text Files.

[gbt02] A. Golbraikh, D. Bonchev, and A. Tropsha, Novel Z/E-Isomerism Descriptors Derived from Molecular Topology and Their Application to QSAR Analysis, J. Chem. Inf. Comput. Sci., 42, 769-787, 2002.

[ghhjs91] J. Gasteiger, B. M. Hendriks, P. Hoever, C. Jochum, and H. Somberg, JCAMP-CS: A Standard Format for Chemical Structure Information in Computer Readable Form, Appl. Spec., 45, 4-11, 1991.

[gm78] J. Gasteiger and M. Marsili, A New Model for Calculating Atomic Charges in Molecules, Tetrahedron Lett., ?, 3181-3184, 1978.

[gt03] A. Golbraikh and A. Tropsha, QSAR Modeling Using Chirality Descriptors Derived from Molecular Topology, J. Chem. Inf. Comput. Sci., 42, 144-154, 2003.

[gxsb00] L. Xue, F. L. Stahura, J. W. Godden, and J. Bajorath, Searching for molecules with similar biological activity: analysis by fingerprint profiling, Pac. Symp. Biocomput., 8, 566-575, 2000.

[lhdl94] P. Lampen, H. Hillig, A. N. Davies, and M. Linscheid, JCAMP-DX for Mass Spectrometry, Appl. Spec., 48, 1545-1552, 1994.

[ml91] E. C. Meng and R. A. Lewis, {D}etermination of {M}olecular {T}opology and {A}tomic {H}ybridisation {S}tates from {H}eavy {A}tom {C}oordinates, J. Comp. Chem., 12, 891-898, 1991.

[mor65] H. L. Morgan, The Generation of a Unique Machine Description for Chemical Structures - A Technique Developed at Chemical Abstracts Service, J. Chem. Doc., 5, 107-113, 1965.

[mr99] P. Murray-Rust and H. S. Rzepa, Chemical Markup, XML, and the Worldwide Web. 1. Basic Principles, J. Chem. Inf. Comput. Sci., 39, 928-942, 1999.

[mr01a] P. Murray-Rust and H. S. Rzepa, Chemical Markup, XML and the World-Wide Web. 2. Information Objects and the CMLDOM, J. Chem. Inf. Comput. Sci., 41, ?-?, 2001.

[mr01b] G. V. Gkoutos, P. Murray-Rust, H. S. Rzepa, and M. Wright, Chemical markup, XML, and the world-wide web. 3. toward a signed semantic chemical web of trust, J. Chem. Inf. Comput. Sci., 41, 1295-1300, 2001.

[msg99] M. C. Hemmer, V. Steinhauer, and J. Gasteiger, Deriving the 3D Structure of Organic Molecules from their Infrared Spectra, Vibrat. Spect., 19, 63-67, 1999.

[sdf] Inc. MDL Information Systems, Structured Data File format.

[smarts] Inc. Daylight Chemical Information Systems, Smiles ARbitrary Target Specification (SMARTS).

[smiles] Inc. Daylight Chemical Information Systems, Simplified Molecular Input Line Entry System (SMILES).

[tc00] R. Todeschini and V. Consonni, 3-52-29913-0, Wiley-VCH, Handbook of Molecular Descriptors.

[wc99] S. A. Wildman and G. M. Crippen, Prediction of Physicochemical Parameters by Atomic Contributions, J. Chem. Inf. Comput. Sci., 39, 868-873, 1999.

[wei88] D. Weinenger, SMILES: a Chemical Language for Information Systems. 1. Introduction to Methodology and Encoding Rules, J. Chem. Inf. Comput. Sci., 28, 31-36, 1988.

[wei89] D. Weinenger, SMILES 2: Algorithm for Generation of Unique SMILES Notation, J. Chem. Inf. Comput. Sci., 29, 97-101, 1989.

[wil01] E. L. Willighagen, Processing CML Conventions in Java, Internet Journal of Chemistry, 4, 4, 2001.

[wy96] W. P. Walters and S. H. Yalkowsky, ESCHER-A Computer Program for the Determination of External Rotational Symmetry Numbers from Molecular Topology, J. Chem. Inf. Comput. Sci., 36, 1015-1017, 1996.

[wz03] J. K. Wegner and A. Zell, Prediction of Aqueous Solubility and Partition Coefficient Optimized by a Genetic Algorithm Based Descriptor Selection Method, J. Chem. Inf. Comput. Sci., 43, 1077-1084, 2003.

[wfz04a] J. K. Wegner, H. Froehlich, and A. Zell, Feature Selection for Descriptor based Classification Models. 1. Theory and GA-SEC Algorithm, J. Chem. Inf. Comput. Sci., 44, ASAP alert, 2004.

[wfz04b] J. K. Wegner, H. Froehlich, and A. Zell, Feature Selection for Descriptor based Classification Models. 2. Human Intestinal Absorption, J. Chem. Inf. Comput. Sci., 44, ASAP alert, 2004.

[zup89] J. Zupan, 0-471-92173-4, Wiley-VCH, Algorithms for Chemists.

PrevHome 
Bibliography  
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Böhm & G. Klebe, Development of New Hydrogen--Bond Descriptors and Their Application to Comparative Molecular Field Analyses , J. Med. Chem., 2002 , 45 , 1585-1597. -Article (bmv84), P. Broto; G. Moreau & C. Vandycke, Molecular Structures: Perception, Autocorrelation Descriptor and SAR Studies , Eur. J. Med. Chem., 1984 , 19 , 66-70. -Book (br90), D. Bonchev & D. H. Rouvray, D. Bonchev & D. H. Rouvray (ed.), Chemical Graph Theory: Introduction and Fundamentals , Gordon and Breach Science Publishers, 1990 , 1. -Article (bs93), B.L.Bush & R.P.Sheridan, PATTY: A Programmable Atom Typer and Language for Automatic Classification of Atoms in Molecular Databases. , J. Chem. Inf. Comput. Sci., 1993 , 33 , 756-762. -Inbook (clr98bfs), T. H. Cormen; C. E. Leiserson & R. L. Rivest, Introduction to Algorithms , 23.2, MIT--Press, 1998 , 469-477. -Inbook (clr98complexity), T. H. Cormen; C. E. Leiserson & R. L. Rivest, Introduction to Algorithms , 2, MIT--Press, 1998 , 23-41. -Inbook (clr98dfs), T. H. Cormen; C. E. Leiserson & R. L. Rivest, Introduction to Algorithms , 23.3, MIT--Press, 1998 , 477-483. -Incollection (dhl90), A.N. Davies; H. Hilling & M. Linscheid, J. Gasteiger (ed.), JCAMP--DX, a standard ? , Springer--Verlag, 1990 , 147-156. -Article (dl93), A. N. Davies & P. Lampen, JCAMP--DX for NMR , Appl. Spec., 1993 , 47 , 1093-1099. -Article (dw88), R. S. Mc Donald & Paul A. Wilks, JCAMP--DX: A Standard Form for Exchange of Infrared Spectra in Computer Readable Form , Appl. Spec., 1988 , 42 , 151-162 . Article (ers00), P. Ertl; B. Rohde & P. Selzer, Fast Calculation of Molecular Polar Surface Area as a Sum of Fragment-Based Contributions and Its Application to the Prediction of Drug Transport Properties , J. Med. Chem. 2000, 43, 3714-3717, 2000 , 43 , 3714-3717. -Article (fig96), J. Figueras, Ring Perception Using Breadth--First Search , J. Chem. Inf. Comput. Sci., 1996 , 36 , 986-991. -Article (ghhjs91), J. Gasteiger; B. M. P. Hendriks; P. Hoever; C. Jochum & H. Somberg, JCAMP--CS: A Standard Format for Chemical Structure Information in Computer Readable Form , Appl. Spec., 1991 , 45 , 4-11. -Article (gm78), J. Gasteiger & M. Marsili, A New Model for Calculating Atomic Charges in Molecules , Tetrahedron Lett., 1978 , 3181-3184. -Article (gmrw01), G. V. Gkoutos; P. Murray--Rust; S. Rzepa & M. Wright, Chemical Markup, XML, and the World--Wide Web. 3. Toward a Signed Semantic Chemical Web of Trust , J. Chem. Inf. Comput. Sci., 2001 , 41 , 1295-1300 . DOI: 10.1021/ci000406v. -Article (gwb98), J. Gillet; P. Willett & J. Bradshaw, Identification of Biological Activity Profiles Using Substructural Analysis and Genetic Algorithms , J. Chem. Inf. Comput. Sci., 1998 , 38 , 165-179. -Article (gxsb00), L. Xue; F. L. Stahura; J. W. Godden & J. Bajorath, Searching for molecules with similar biological activity: analysis by fingerprint profiling , Pac. Symp. Biocomput., 2000 , 8 , 566-575. -Misc (jwd00), C. A. James; D. Weininger & J. Delany, Daylight Theory Manual. -Article (lhdl94), P. Lampen; H. Hillig; A. N. Davies & Michael Linscheid, JCAMP--DX for Mass Spectrometry , Appl. Spec., 1994 , 48 , 1545-1552. -Article (lldf01), C. A. Lipinski; F. Lombardo; B. W. Dominy & P. J. Feeney, Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings , Adv. Drug Delivery Reviews, 2001 , 46 , 3-26. -Misc (mdlMolFormat), MDL Information Systems, Inc., MDL CTfile Formats. -Article (ml91), E. C. Meng & R. A. Lewis, Determination of Molecular Topology and Atomic Hybridisation States from Heavy Atom Coordinates , J. Comp. Chem., 1991 , 12 , 891-898. -Article (mor65), H. L. Morgan, The Generation of a Unique Machine Description for Chemical Structures -- A Technique Developed at Chemical Abstracts Service. , J. Chem. Doc., 1965 , 5 , 107-113. -Article (mr01), P. Murray--Rust & H. S. Rzepa, Chemical Markup, XML and the World--Wide Web. 2. Information Objects and the CMLDOM , J. Chem. Inf. Comput. Sci., 2001 , 41 , 1113-1123 . DOI: 10.1021/ci000404a. -Article (mr03), P. Murray--Rust & H. S. Rzepa, Chemical Markup, XML and the World--Wide Web. 4. CML Schema , J. Chem. Inf. Comput. Sci., 2003 , 43 , 757-772 . DOI: 10.1021/ci0256541. -Article (mrww04), P. Murray--Rust; H. S. Rzepa; J. Williamson & E. L. Willighagen, Chemical Markup, XML and the World--Wide Web. 5. Applications of Chemical Metadata in RSS Aggregators , J. Chem. Inf. Comput. Sci., 2004 , 44 , 462-469 . DOI: 10.1021/ci034244p. -Article (odtl01), T. I. Oprea; A. M. Davis; S. J. Teague & P. D. Leeson, Is There a Difference between Leads and Drugs? A Historical Perspective , J. Chem. Inf. Comput. Sci., 2001 , 41 , 1308-1315 . DOI: 10.1021/ci010366a. -Misc (pdbFormat), Protein Data Bank (PDB) File Format , 2002. -Misc (povray), POV--Team, Persistence of Vision Raytracer (POVRay). -Article (rr99b), P. Murray--Rust & H. S. Rzepa, Chemical Markup, XML, and the Worldwide Web. 1. Basic Principles , J. Chem. Inf. Comput. Sci., 1999 , 39 , 928-942 . DOI: 10.1021/ci990052b. -Manual (smarts), Daylight Chemical Information Systems, Inc., Smiles ARbitrary Target Specification (SMARTS). -Manual (smilesFormat), Daylight Chemical Information Systems, Inc., Simplified Molecular Input Line Entry System (SMILES). -Manual (sybylmol2), Tripos, Tripos Mol2 File Format. -Inbook (tc00kiershape), R. Todeschini & V. Consonni, Handbook of Molecular Descriptors , K, Wiley--VCH, 2000 , 248-250. -Inbook (tc00zagrebgroup), R. Todeschini & V. Consonni, Handbook of Molecular Descriptors , Z, Wiley--VCH, 2000 , 509. -Book (tri92), N. Trinajsti, Chemical Graph Theory , CRC Press, Florida, U.S.A., 1992. -Article (wc99), S. A. Wildman & G. M. Crippen, Prediction of Physicochemical Parameters by Atomic Contributions , J. Chem. Inf. Comput. Sci., 1999 , 39 , 868-873. -Article (wei88), D. Weininger, SMILES, a Chemical Language for Information Systems. 1. Introduction to Methodology and Encoding Rules. , J. Chem. Inf. Comput. Sci., 1988 , 28 , 31-36. -Article (wfz04a), Wegner, J. K.; Fröhlich, H. & Zell, A., Feature selection for Descriptor based Classification Models. 1. Theory and GA--SEC Algorithm , J. Chem. Inf. Comput. Sci., 2004 , 44 . DOI: 10.1021/ci0342324. -Article (wfz04b), J. K. Wegner; H. Fröhlich & A. Zell, Feature selection for Descriptor based Classification Models. 2. Human Intestinal Absorption (HIA) , J. Chem. Inf. Comput. Sci., 2004 , 44 . DOI: 10.1021/ci034233w. -Article (wil01), E. L. Willighagen, Processing CML Conventions in Java , Internet Journal of Chemistry, 2001 , 4 , 4. -Article (www89), D. Weininger; A. Weininger & J. L. Weininger, Algorithm for generation of unique SMILES notation , J. Chem. Inf. Comput. Sci., 1989 , 29 , 97-101. -Article (wy96), W. P. Walters & S. H. Yalkowsky, ESCHER--A Computer Program for the Determination of External Rotational Symmetry Numbers from Molecular Topology , J. Chem. Inf. Comput. Sci., 1996 , 36 , 1015-1017. -Article (wz03), Wegner, J. K. & Zell, A., Prediction of Aqueous Solubility and Partition Coefficient Optimized by a Genetic Algorithm Based Descriptor Selection Method , J. Chem. Inf. Comput. Sci., 2003 , 43 , 1077-1084 . DOI: 10.1021/ci034006u. -Inbook (zup89c), J. Zupan, Algorithms for Chemists , Wiley, 1989 , 102-142 . \ No newline at end of file diff --git a/java/docs/literature.tex b/java/docs/literature.tex deleted file mode 100644 index 1befd3f..0000000 --- a/java/docs/literature.tex +++ /dev/null @@ -1,34 +0,0 @@ -% -% Filename: $RCSfile: literature.tex,v $ -% Authors: Joerg Wegner -% Version: $Revision: 1.1.1.1 $ -% $Date: 2004/12/06 15:33:07 $ -% $Author: wegner $ -% Copyright (c) Joerg Wegner; CCC Computer Chemistry Center, Germany -% -% ------------------------------------------------------------------------ -% AMS-LaTeX Bibliography ************************************************* -% ------------------------------------------------------------------------ -\documentclass[11pt]{amsart} -\usepackage[inactive]{srcltx} -% **** ------------------------------------------------------------------- -\vfuzz1pc % Don't bother to report overfull boxes if over-edge is < 1pc -\hfuzz1pc % Don't bother to report overfull boxes if over-edge is < 1pc - -%------------------------------------------------------------------------------------------- -% JUST FOR TTH USERS !;-) -%------------------------------------------------------------------------------------------- -%%tth:\begin{html}Literature JOELib, J.K. Wegner, 2003\end{html} -%%tth:\begin{html}\end{html} -%------------------------------------------------------------------------------------------- - -%%% TITLE ---------------------------------------------------------------- -%%% ---------------------------------------------------------------------- -\begin{document} -% ------------------------------------------------------------------------ -\nocite{*} -% ------------------------------------------------------------------------ -\bibliographystyle{angewandte_chemie} -\bibliography{literature} -\end{document} -% ------------------------------------------------------------------------ -- cgit v1.2.3